Historical Introgression from Wild Relatives Enhanced Climatic Adaptation and Resistance to Pneumonia in Sheep

Cao, Yin-Hong; Xu, Song-Song; Shen, Min; Chen, Zehui; Gao, Lei; Lv, Feng‐Hua; Xie, Xinglong; Wang, Xinhua; Yang, Hua; Liu, Changbin; Zhou, Ping; Wan, Pengcheng; Zhang, Yunsheng; Yang, Jingquan; Pi, Wen-Hui; Hehua, EEr; Berry, D.P.; Barbato, Mario; Esmailizadeh, Ali; Nosrati, Maryam; Salehian-Dehkordi, Hosein; Dehghani-Qanatqestani, Mostafa; Dotsev, Arsen V; Deniskova, Tatiana; Zinovieva, N. A.; Brem, Gottfried; Štěpánek, Ondřej; Ciani, Elena; Weimann, Christina; Erhardt, G.; Mwacharo, Joram M.; Ahbara, Abulgasim; Han, Jianlin; Hanotte, Olivier; Miller, Joshua M.; Sim, Zijian; Coltman, David W.; Kantanen, Juha; Bruford, Michael William; Lenstra, Johannes A.; Kijas, James W.; Li, Menghua

doi:10.1093/molbev/msaa236

Cited by 65 publications

(84 citation statements)

References 83 publications

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“…We combined the genotypes of Ovine Infinium HD (600K) SNP BeadChip in 2059 individuals from 67 populations all over the world, a large majority of which are from our research group ( Kijas et al, 2014 ; Ren et al, 2016 ; Xu et al, 2017 ; Peng et al, 2017 ; Zhao et al, 2017 ; Gao et al, 2018 ; Xu et al, 2018 ; Rochus et al, 2018 ; Cao et al, 2020 ) ( Figure 1A and Supplementary Table 1 ). We updated all the SNP positions in the BeadChip based on the sheep reference assembly Oar_v.4.0 1 .…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Detection of Copy Number Variations and Their Association With Distinct Phenotypes in the World’s Sheep

Salehian-Dehkordi

et al. 2021

Front. Genet.

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Copy number variations (CNVs) are a major source of structural variation in mammalian genomes. Here, we characterized the genome-wide CNV in 2059 sheep from 67 populations all over the world using the Ovine Infinium HD (600K) SNP BeadChip. We tested their associations with distinct phenotypic traits by conducting multiple independent genome-wide tests. In total, we detected 7547 unique CNVs and 18,152 CNV events in 1217 non-redundant CNV regions (CNVRs), covering 245 Mb (∼10%) of the whole sheep genome. We identified seven CNVRs with frequencies correlating to geographical origins and 107 CNVRs overlapping 53 known quantitative trait loci (QTLs). Gene ontology and pathway enrichment analyses of CNV-overlapping genes revealed their common involvement in energy metabolism, endocrine regulation, nervous system development, cell proliferation, immune, and reproduction. For the phenotypic traits, we detected significantly associated (adjusted P < 0.05) CNVRs harboring functional candidate genes, such as SBNO2 for polycerate; PPP1R11 and GABBR1 for tail weight; AKT1 for supernumerary nipple; CSRP1, WNT7B, HMX1, and FGFR3 for ear size; and NOS3 and FILIP1 in Wadi sheep; SNRPD3, KHDRBS2, and SDCCAG3 in Hu sheep; NOS3, BMP1, and SLC19A1 in Icelandic; CDK2 in Finnsheep; MICA in Romanov; and REEP4 in Texel sheep for litter size. These CNVs and associated genes are important markers for molecular breeding of sheep and other livestock species.

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Section: Methodsmentioning

confidence: 99%

Genome-Wide Detection of Copy Number Variations and Their Association With Distinct Phenotypes in the World’s Sheep

Salehian-Dehkordi

et al. 2021

Front. Genet.

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“…This could identify the key genes controlling the investigated traits. With advancements in genomic research technologies, the understanding of genetic bases underlying evolutionally and agriculturally valuable traits has drastically increased (Kijas et al 2012;Jiang et al 2014;Lv et al 2014Lv et al , 2015Yang et al 2016;Zhao et al 2017;Naval-Sanchez et al 2018;Pan et al 2018;Hu et al 2019;Cao et al 2021). Since 2012, various genomic-based studies have been conducted to understand the genetic basis and genomic architecture of sheep tails and to find the specific causal genomic variant(s) contributing to sheep tail patternmaking (Moradi et al 2012;Moioli et al 2015;Wei et al 2015;Pan et al 2019;Dong et al 2020b;Li et al 2020b;Shao et al 2020;Luo et al 2021) (Fig.…”

Section: Telling the Tale Of Tail In Sheep: Genomic Insightsmentioning

confidence: 99%

Trends towards revealing the genetic architecture of sheep tail patterning: Promising genes and investigatory pathways

et al. 2021

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Different sheep breeds have evolved after initial domestication, generating various tail phenotypic patterns. The phenotypic diversity of sheep tail patterns offers ideal materials for comparative analysis of its genetic basis. Evolutionary biologists, animal geneticists, breeders, and producers have been curious to clearly understand the underlying genetics behind phenotypic differences in sheep tails. Understanding the causal gene(s) and mutation (s) underlying these differences will help probe an evolutionary riddle, improve animal production performance, promote animal welfare, and provide lessons that help comprehend human diseases related to fat deposition (i.e., obesity). Historically, fat tails have served as an adaptive response to aridification and climate change. However, the fat tail is currently associated with compromised mating and animal locomotion, fat distribution in the animal body, increased raising costs, reduced consumer preference, and other animal welfare issues such as tail docking. The developing genomic approaches provide unprecedented opportunities to determine causal variants underlying phenotypic differences among populations. In the last decade, researchers have performed several genomic investigations to assess the genomic causality underlying phenotypic variations in sheep tails. Various genes have been suggested with the prominence of several potentially significant causatives, including the BMP2 and PDGFD genes associated with the fat tail phenotype and the TBXT gene linked with the caudal vertebrae number and tail length. Although the potential genes related to sheep tail characteristics have been revealed, the causal variant(s) and mutation(s) of these high-ranking candidate genes are still elusive and need further investigation. The review discusses the potential genes, sheds light on a knowledge gap, and provides possible investigative approaches that could help determine the specific genomic causatives of sheep tail patterns. Besides, characterizing and revealing the genetic determinism of sheep tails will help solve issues compromising sheep breeding and welfare in the future.

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“…Tajima's D statistic (See Box 4) has been used to analyse wild and domestic sheep data to identify a genomic region involved in the resistance to pneumonia [143]. A scan of Russian cattle genomes using Tajima's D statistic detected signatures of selection most likely resulting from adaptation to cold environments [144].…”

Section: Selection Signaturesmentioning

confidence: 99%

“…LAI has been widely applied to identify adaptive introgression related to climatic stressors in livestock. Adaptive introgression from wild to domestic sheep of loci affecting climatic adaptation and resistance to pneumonia has been identified using LAI [143,199]. Using LAI and multiple-reference adjustments, ancestry components of indicine origin were found in cattle breeds from Central Italy that are associated with resilience to harsh environments and climatic conditions [200].…”

Section: Local Ancestry Inferencementioning

confidence: 99%

The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock

Passamonti

Somenzi

Barbato

et al. 2021

Animals

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Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.

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Historical Introgression from Wild Relatives Enhanced Climatic Adaptation and Resistance to Pneumonia in Sheep

Cited by 65 publications

References 83 publications

Genome-Wide Detection of Copy Number Variations and Their Association With Distinct Phenotypes in the World’s Sheep

Genome-Wide Detection of Copy Number Variations and Their Association With Distinct Phenotypes in the World’s Sheep

Trends towards revealing the genetic architecture of sheep tail patterning: Promising genes and investigatory pathways

The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock

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